Is the purpose cartographic or analytic? If it's cartographic, it would be a bad idea to actually change the underlying data in order to achieve a particular mode of rendering them: knowing that would suggest purely cartographic solutions. If it's analytic, would you mind telling us what kind of analysis these changes are intended to support? (In effect it looks like you are asking to destroy information about connectivity, which is an unusual and curious thing to do.)
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whuber♦Jan 17 '13 at 20:12

@whuber It is for analytic purpose. Once the empty space is defined, I will feed the shapefile to a simulator which will be configured to identify them as intersection.
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SibiJan 17 '13 at 21:17